refactor(validation): use ml_id as primary ID, add chembl_id field

validation_output/README.md

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+# MacrolactoneDB Validation Output
+
+This directory contains validation results for MacrolactoneDB 12-20 membered rings.
+
+## Directory Structure
+
+```
+validation_output/
+├── README.md                    # This file
+├── fragments.db                 # SQLite database with all data
+├── summary.csv                  # Summary of all processed molecules
+├── summary_statistics.json      # Statistical summary
+│
+├── ring_size_12/                # 12-membered rings
+├── ring_size_13/                # 13-membered rings
+...
+└── ring_size_20/                # 20-membered rings
+    ├── molecules.csv            # Molecules in this ring size
+    ├── standard/                # Standard macrolactones
+    │   ├── numbered/            # Numbered ring images
+    │   │   └── {id}_numbered.png
+    │   └── sidechains/          # Fragment images
+    │       └── {id}/
+    │           └── {id}_frag_{n}_pos{pos}.png
+    ├── non_standard/            # Non-standard macrocycles
+    │   └── original/
+    │       └── {id}_original.png
+    └── rejected/                # Not macrolactones
+        └── original/
+            └── {id}_original.png
+```
+
+## Database Schema
+
+### Tables
+
+- **parent_molecules**: Original molecule information
+- **ring_numberings**: Ring atom numbering details
+- **side_chain_fragments**: Fragmentation results with isotope tags
+- **validation_results**: Manual validation records
+
+### Key Fields
+
+- `classification`: standard_macrolactone | non_standard_macrocycle | not_macrolactone
+- `dummy_isotope`: Cleavage position stored as isotope value for reconstruction
+- `cleavage_position`: Position on ring where side chain was attached
+
+## Ring Numbering Convention
+
+1. Position 1 = Lactone carbonyl carbon (C=O)
+2. Position 2 = Ester oxygen (-O-)
+3. Positions 3-N = Sequential around ring
+
+## Isotope Tagging
+
+Fragments use isotope values to mark cleavage position:
+- `[5*]CCO` = Fragment from position 5, dummy atom has isotope=5
+- This enables precise reconstruction during reassembly
+
+## CSV Columns
+
+### summary.csv
+
+- `source_id`: Original molecule ID from MacrolactoneDB
+- `classification`: Classification result
+- `ring_size`: Detected ring size (12-20)
+- `num_sidechains`: Number of side chains detected
+- `cleavage_positions`: JSON array of cleavage positions
+- `processing_status`: pending | success | failed | skipped
+
+## Querying the Database
+
+```bash
+# List tables
+sqlite3 fragments.db ".tables"
+
+# Get standard macrolactones with fragments
+sqlite3 fragments.db "SELECT * FROM parent_molecules WHERE classification='standard_macrolactone' LIMIT 5;"
+
+# Get fragments for a specific molecule
+sqlite3 fragments.db "SELECT * FROM side_chain_fragments WHERE parent_id=1;"
+
+# Count by ring size
+sqlite3 fragments.db "SELECT ring_size, COUNT(*) FROM parent_molecules GROUP BY ring_size;"
+```

validation_output/summary_statistics.json

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+{
+  "total_molecules": 1097,
+  "by_classification": {
+    "non_standard_macrocycle": 617,
+    "standard_macrolactone": 459,
+    "not_macrolactone": 21
+  },
+  "by_ring_size": {
+    "14.0": 301,
+    "16.0": 187,
+    "15.0": 161,
+    "12.0": 141,
+    "19.0": 85,
+    "18.0": 80,
+    "13.0": 67,
+    "20.0": 24,
+    "17.0": 19
+  },
+  "by_status": {
+    "skipped": 638,
+    "success": 367,
+    "failed": 92
+  }
+}